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23.1.0 release candidate 0

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@mgxd mgxd released this 13 Jul 19:31
· 353 commits to master since this release
23.1.0rc0
86ab4ec

Release Notes

A release candidate of the next minor release of NiBabies, this release includes a number of new goodies, including:

New surface reconstruction option

M-CRIB-S (Adamson et al., https://www.nature.com/articles/s41598-020-61326-2), has shown to improve performance in participants under 9 months. If you would like to try this method, add the following to your command: --surface-recon-method mcribs.

Note: Currently, a pre-computed segmentation derivative must be provided to run mcribs.

Improved batch processing

NiBabies now automatically parses the BIDS directory for participant ages, first searching in the
participant's session.tsv, and falling back to participants.tsv. This simplifies batch submissions including multiple subjects & sessions. As a result, the --age-months flag has been deprecated, and will be removed in a later release.

Augmented surface projection

An option to determine and exclude high-variance voxels from being projected to the surface when creating CIFTI files. To enable this, add --project-goodvoxels to your command.

  • CI: Purge codecov python package (#282)
  • DKR: Upgrade Docker base, c3d (#275)
  • DKR: Add M-CRIB-S to Docker container (#283)
  • DKR: Update dependencies, split into multi-stage build
  • ENH: Add option to exclude projecting high variance voxels to surface (#278)
  • ENH: Resample morphometrics to fsLR CIFTI-2 files when outputing CIFTIs (#279)
  • ENH: Add MCRIBReconAll as alternative surface reconstruction method (#283)
  • ENH: Reorder anatomical processsing, run ANTs DenoiseImage on anatomicals (#286)
  • ENH: Extract participant ages from BIDS sources, deprecate --age-months (#287)
  • ENH: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2star map estimation (#296)
  • FIX: Improve free memory estimation (#284)
  • FIX: Ensure age is extracted from sessions file (#291)
  • FIX: Restore CIFTI medial wall masking, subcortical volume LAS reorientation (#298)
  • FIX: Recify "goodvoxels" surface projection (#301)
  • MAINT: Drop TemplateFlowSelect patches (#290)
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